if your mobo uses intel matrix storage or nvidia media shield, the raid is hardware based.

windows provides built-in mirroring (raid-1), spanning (jbod), and striping (raid-0) using dynamic volumes, but the boot drive can't be striped. also, dynamic volumes will not perform as well a hardware raid array.

as for mobo-based raid, you can use a striped array as a boot device. but unless you're using old/cheap SSDs, you probably won't get much benefit from striping since most newer SSDs can already utilize 80% of the read bandwidth of many SATA controllers. and, you'll likely lose TRIM support (which is vital to keep SSDs at top performance) since the OS will communicating with the raid controller and not the SSDs.

if you're still determined to stripe your SSDs with your mobo raid, create the array first, then use cloning software to transfer the drive image from your existing boot device to the new array.